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Erin Doyle

Biology - Assistant Professor
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B.S. in Applied Mathematics
The University of Tulsa, 2007

Ph.D. in Bioinformatics and Computational Biology
Iowa State University, 2013

Courses Taught

Inquiry Lab (SEA-Phages), Energy of Life: Cells to Ecosystems, Genetics, Biology Research I

Teaching Interests

My teaching interests center on introducing computational and mathematical thinking into the core Biology curriculum. The recent explosion of gene and genome sequence data has made it impossible for biologists to effectively mine all of the available data without the aid of computers and sophisticated mathematical models! My goal is to help my students understand the importance of mathematics, computer science, and statistics to modern biology. In addition to developing classroom activities to give students hands-on experience using common computational tools and biological databases, I hope to interest students in the algorithms and models that make these tools work. I am also interested in developing stand-alone upper level courses in bioinformatics and computational biology that would allow students to explore this kind of science in and in-depth way.

Research Interests

My previous research has focused on the analysis of whole genome sequences to identify binding sites for a specific type of DNA binding protein called a TAL effector. TAL effectors come from bacteria that cause diseases in a variety of economically important crops, and understanding how these proteins bind to DNA has implications for understanding crop diseases and disease resistance. TAL effectors can also be used for editing DNA sequences in living cells and organisms, making them potentially useful in genome engineering applications and for therapies for genetic diseases. My research program at Doane will continue to build on my experience in analyzing genome sequence data for TAL effector binding sites, and in using genome sequence data to understand crop disease resistance. More generally, research in my lab will allow students to gain experience using computational approaches to generate experimentally testable hypotheses and then use those experimental results to refine computational models of biological processes.


**Cernadas, R.A., Doyle, E.L., Niño –Liu, D.O., Wilkins, K.E., Bancroft, T., Wang, L., Schmidt, C.L., Caldo, R.A., Yang, B., White, F.F., Nettleton, D., Wise, R.P., and Bogdanove, A.J. (2014). Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene. Accepted for publication in PLoS Pathogens.

**Doyle, E.L., Hummel, A.W., Demorest, Z.L., Starker, C.G., Voytas, D.F., Bradley, P., and Bogdanove, A.J. (2013) TAL Effector specificity for base 0 of the DNA target is altered in a complex, cffector- and assay-dependent manner by substitutions for the tryptophan in cryptic repeat –1. PLoS One, 8, e82120.

Doyle, E.L., Stoddard, B.L., Voytas, D.F., and Bogdanove, A.J. (2013). TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA targeting proteins. Trends in Cell Biology, 23, 390-398.

Hummel, A.W., Doyle, E.L. and Bogdanove, A.J. (2012) Addition of transcription activator-like effector binding sites to a pathogen strain-specific rice bacterial blight resistance gene makes it effective against additional strains and against bacterial leaf streak. The New Phytologist, 195, 883-893.

Doyle, E.L., Booher, N.J., Standage, D.S., Voytas, D.F., Brendel, V.P., VanDyk, J.K. and Bogdanove, A.J. (2012) TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. Nucleic Acids Research, 40, W117-W122.

Cermak, T.*, Doyle, E.L.* (*co-first authors), Christian, M., Wang, L., Zhang, Y., Schmidt, C., Baller, J.A., Somia, N.V., Bogdanove, A.J. and Voytas, D.F. (2011) Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Research, 39, e82.

Vendettuoli, M., Doyle, E. and Hofmann, H. (2011) In Arabnia, H. R. and Tran, Q. N. (eds.), Software Tools and Algorithms for Biological Systems. Springer-Verlag Berlin, pp. 145-153.

Christian, M., Cermak, T., Doyle, E.L., Schmidt, C., Zhang, F., Hummel, A., Bogdanove, A.J. and Voytas, D.F. (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics, 186, 757-761.

** indicates published while at Doane College